TY - JOUR T1 - Y chromosomal noncoding RNA regulates autosomal gene expression via piRNAs in mouse testis JF - bioRxiv DO - 10.1101/285429 SP - 285429 AU - Hemakumar M. Reddy AU - Rupa Bhattacharya AU - Zeenath Jehan AU - Kankadeb Mishra AU - Pranatharthi Annapurna AU - Shrish Tiwari AU - Nissankararao Mary Praveena AU - Jomini Liza Alex AU - Vishnu M Dhople AU - Lalji Singh AU - Mahadevan Sivaramakrishnan AU - Anurag Chaturvedi AU - Nandini Rangaraj AU - Shiju Michael Thomas AU - Badanapuram Sridevi AU - Sachin Kumar AU - Ram Reddy Dereddi AU - Sunayana Rayabandla AU - Rachel A. Jesudasan Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/03/24/285429.abstract N2 - Repeats from the male-specific long arm of mouse Y-chromosome (MSYq) transcribe protein coding and noncoding RNAs. Majority of genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility and sterility, depending on the length of deletion. The connection between Yq deletion and autosomal gene regulation was not well studied before. We describe a novel multi-copy mouse Yq-derived long noncoding RNA, Pirmy (piRNA from mouse Y chromosome), which shows unprecedented alternative splicing in testis. Further, Pirmy acts as a template for several piRNAs in mouse testis. Mice with deletions of Yq including the region of Pirmy exhibit differential male fertility, aberrant sperm morphology, motility and sex ratio skewed towards females. We identified deregulation of ten autosome-encoded sperm proteins in a Y-deleted strain of mouse. Pirmy splice variants have homology to 5’/3’ UTRs of these deregulated autosomal genes. Thus, subfertility in Y-deleted mice appears to be a polygenic phenomenon that is partially regulated epistatically by the Y-encoded Pirmy. Our study provides novel and interesting insights into possible role of MSY-derived noncoding RNAs in male fertility and reproduction. Finally, sperm phenotypes from Y-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of Y-derived noncoding RNAs in male sterility and speciation.Significance Our study adds new dimensions to the repertoire of functions that Y-heterochromatin has with respect to autosomal gene regulation in male fertility. We describe a novel sex and species-specific ncRNA, Pirmy, transcribed from mouse Y-chromosome, with unprecedented alternative splicing. Mice with deletions of Y-long arm (Yq) were reported to exhibit differential sterility and sperm abnormalities. We identify sperm proteins that are deregulated in Yq-deleted mice; corresponding genes map to autosomes and display sequence homology to piRNAs derived from Pirmy in their UTRs. Thus, piRNAs from species-specific repeats appear to regulate autosomal genes involved in reproduction. The male sterility phenotypes of Yq-deleted mice and cross-species hybrids are comparable, indicating a larger role for species-specific repeats from Y-chromosome in speciation and evolution. ER -